Merge branch 'topic/default/add-sample-wake_legi' into 'branch/default'

Performance optimizations for PIV

See merge request fluiddyn/fluidimage!94

CHANGES.md

@@ -3,6 +3,10 @@
 See also the
 [unreleased changes](https://foss.heptapod.net/fluiddyn/fluidimage/-/compare/0.4.3...branch%2Fdefault).
 
+## [0.4.5] (2024-04-17)
+
+- Performance optimizations for PIV (- ~40% of CPU time without TPS)
+
 ## [0.4.4] (2024-04-16)
 
 - `fluidimage-monitor` [Textual](https://textual.textualize.io/) app to monitor

doc/examples/profile_piv_work.py

@@ -0,0 +1,63 @@
+"""Profile PIV work with pyinstrument
+
+Result with fluidimage 0.4.4:
+
+total: ~4.7 s
+
+- ~25% _compute_indices_max, fluidimage/calcul/correl.py:78
+- ~25% CorrelFFTW.__call__,  fluidimage/calcul/correl.py:690  (10.4% fftshift, ~1% fft)
+- ~10% WorkPIVFromDisplacement._crop_im0 (and 1) fluidimage/works/piv/singlepass.py:403
+- ~17% smooth_clean   fluidimage/calcul/smooth_clean.py:25    (9% griddata)
+
+"""
+
+import os
+
+from pyinstrument import Profiler
+from pyinstrument.renderers import ConsoleRenderer
+
+from fluidimage.piv import Work
+
+os.environ["OMP_NUM_THREADS"] = "1"
+
+params = Work.create_default_params()
+
+params.series.path = "../../image_samples/wake_legi/images/B*.png"
+
+params.piv0.shape_crop_im0 = 40
+params.piv0.displacement_max = 14
+
+params.piv0.nb_peaks_to_search = 2
+params.piv0.particle_radius = 3
+
+params.mask.strcrop = ":, :1500"
+
+params.multipass.number = 2
+
+params.multipass.use_tps = "last"
+# params.multipass.use_tps = False
+params.multipass.subdom_size = 200
+params.multipass.smoothing_coef = 10.0
+params.multipass.threshold_tps = 0.5
+
+params.fix.correl_min = 0.15
+params.fix.threshold_diff_neighbour = 3
+
+work = Work(params=params)
+
+profiler = Profiler()
+profiler.start()
+piv = work.process_1_serie()
+profiler.stop()
+
+print(
+    profiler.output(
+        renderer=ConsoleRenderer(
+            unicode=True,
+            color=True,
+            show_all=False,
+            # time="percent_of_total",
+            # flat=True,  # buggy with pyinstrument 4.6.2!
+        )
+    )
+)

doc/examples/test_run_examples.py

@@ -46,6 +46,7 @@ def teardown_module(module):
         "surface_tracking.py",
         "preproc_sback1_filter.py",
         "preproc_sback2_rescale.py",
+        "profile_piv_work.py",
     ]
 )
 

pixi.toml

@@ -37,3 +37,5 @@ pythran = ">=0.15.0"
 pytest = ">=8.0.0"
 pytest-cov = ">=4.1.0"
 coverage = ">=7.4.1"
+pytest-asyncio = ">=0.23.6,<0.24"
+linkify-it-py = ">=2.0.3,<2.1"

pyproject.toml

@@ -9,7 +9,7 @@ build-backend = 'mesonpy'
 
 [project]
 name = "fluidimage"
-version = "0.4.4"
+version = "0.4.5"
 description = "Fluid image processing with Python."
 authors = [
     {name = "Pierre Augier", email = "[email protected]"},
@@ -64,7 +64,7 @@ pims = ["pims"]
 opencv = ["opencv-python"]
 graph = ["gprof2dot"]
 pytest = ["pytest", "pytest-asyncio"]
-all = ["fluidimage[pims, opencv-python, gprof2dot, pytest]"]
+all = ["fluidimage[pims, opencv, graph, pytest]"]
 # qt = ["PySide6"]
 
 [project.entry-points."fluidimage.executors"]
@@ -124,6 +124,7 @@ dev = [
     "isort",
     "ipdb>=0.13.13",
     "textual-dev",
+    "pyinstrument",
 ]
 
 [tool.pdm.scripts]

src/fluidimage/calcul/_evaluate_subpix.py

@@ -23,11 +23,6 @@
 except ImportError:
     classes.pop("skcufft")
 
-try:
-    import theano
-except ImportError:
-    classes.pop("theano")
-
 
 def setUpImages(nx, ny, dx, dy, part_size):
     displacements = np.array([dx, dy])